5C9M

The structure of oxidized rat cytochrome c (T28A) at 1.362 angstroms resolution.

• PDB DOI: https://doi.org/10.2210/pdb5C9M/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-06-28 Released: 2016-09-21 
• Deposition Author(s): Edwards, B.F.P., Mahapatra, G., Vaishnav, A.A., Brunzelle, J.S., Huttemann, M.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free: 0.170 
• R-Value Work: 0.129 
• R-Value Observed: 0.131 

Starting Model: experimental

Literature

The structure of oxidized rat cytochrome c (T28A) at 1.362 angstroms resolution.

Edwards, B.F.P., Mahapatra, G., Vaishnav, A.A., Brunzelle, J.S., Huttemann, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 49.72 kDa 
• Atom Count: 3,944 
• Modelled Residue Count: 416 
• Deposited Residue Count: 420 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c, somatic	A, B, C, D	105	Rattus norvegicus	Mutation(s): 1  Gene Names: Cycs
UniProt
Find proteins for P62898 (Rattus norvegicus) Explore P62898  Go to UniProtKB:  P62898

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEC	E [auth A], G [auth B], J [auth C], L [auth D]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N
FC6	F [auth A], H [auth B], I [auth B], K [auth C]	HEXACYANOFERRATE(3-) C6 Fe N6 HCMVSLMENOCDCK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free: 0.170 
• R-Value Work: 0.129 
• R-Value Observed: 0.131 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.517	α = 109.86
b = 52.567	β = 92.93
c = 61.771	γ = 92.2

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	phasing
Aimless	data scaling
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-09-21 
Deposition Author(s): Edwards, B.F.P., Mahapatra, G., Vaishnav, A.A., Brunzelle, J.S., Huttemann, M.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	NIGMS RO1 089900

Revision History  

• Version 1.0: 2016-09-21
  Type: Initial release
  
• Version 1.1: 2017-09-06
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2017-11-01
  Changes: Author supporting evidence
• Version 1.3: 2019-12-25
  Changes: Author supporting evidence, Derived calculations
• Version 1.4: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-10-23
  Changes: Structure summary